Contacts of the helix formed by residues 26 - 40 (chain A) in PDB entry 1HMU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A THR* 1.3 65.5 + - - -
28A ALA* 3.5 2.5 - - - -
29A GLU* 3.8 13.0 + - - +
30A LEU* 3.3 21.1 + - - +
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLY* 1.3 69.8 - - - -
28A ALA* 1.3 67.0 + - - +
30A LEU* 3.1 8.8 + - - +
31A ILE* 2.9 41.7 + - + +
193A GLU* 5.8 2.0 - - - -
196A LEU* 5.9 0.2 - - + -
252A THR* 4.0 19.9 - - + -
253A PRO* 4.4 12.4 - - + +
254A TYR* 4.0 19.3 - - + -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY* 4.5 0.4 - - - -
27A THR* 1.3 81.5 - - - +
29A GLU* 1.3 58.3 + - - +
31A ILE* 3.3 5.5 + - - +
32A MET* 2.9 30.5 + - - +
188A LEU* 3.9 25.1 - - + +
191A SER* 6.0 3.8 - - - +
193A GLU* 3.9 27.6 + - - +
196A LEU* 5.1 2.9 - - + -
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY* 3.8 14.8 + - - +
27A THR 3.2 0.4 - - - -
28A ALA* 1.3 78.6 - - - +
30A LEU* 1.3 57.5 + - - +
32A MET* 3.4 6.9 + - - +
33A LYS* 2.9 30.6 + - + +
145A ARG* 4.1 18.3 + - - -
146A TYR* 3.1 30.7 + - - -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY 3.3 11.6 + - - +
27A THR* 3.1 13.1 + - - +
29A GLU* 1.3 79.5 - - - +
31A ILE* 1.3 62.7 + - - +
33A LYS* 3.4 10.3 + - + +
34A ARG* 3.2 60.5 + - + +
251A ASP 5.2 3.1 - - - +
252A THR* 4.5 15.5 - - + -
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Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 2.9 36.0 + - + +
28A ALA* 3.7 6.5 - - - +
30A LEU* 1.3 76.1 - - + +
32A MET* 1.3 64.4 + - - +
34A ARG* 3.0 15.1 + - - +
35A VAL* 3.0 12.0 + - - +
184A PHE* 3.5 33.9 - - + -
188A LEU* 4.0 8.3 - - + -
196A LEU* 4.7 11.7 - - + -
248A TYR* 3.7 26.9 - - + +
249A VAL* 4.0 18.6 - - + -
252A THR* 4.5 9.9 - - + +
254A TYR* 4.2 14.4 - - + -
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Residues in contact with MET 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA 2.9 17.8 + - - +
29A GLU* 3.7 10.1 - - - +
31A ILE* 1.3 74.2 - - - +
33A LYS* 1.3 67.1 + - - +
35A VAL* 3.0 9.6 + - - +
36A MET* 2.9 20.6 + - - +
142A ILE* 3.9 18.8 - - + +
145A ARG* 2.9 41.7 - - - +
146A TYR* 3.4 13.2 + - + +
188A LEU* 3.0 58.3 - - + +
189A LEU* 3.4 13.0 - - + +
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLU* 2.9 20.5 + - + +
30A LEU* 3.4 12.6 - - + +
32A MET* 1.3 78.3 - - - +
34A ARG* 1.3 65.2 + - + +
36A MET* 3.2 35.5 + - + +
37A LEU* 3.0 40.6 + - + +
146A TYR* 3.2 25.7 + - + +
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.2 46.0 + - + +
31A ILE* 3.0 8.3 + - - +
33A LYS* 1.3 76.4 - - + +
35A VAL* 1.3 66.0 + - - +
37A LEU* 3.4 11.0 + - + +
38A ASP* 3.0 23.6 + - - +
247A ASN* 4.0 8.9 + - - +
248A TYR* 2.9 38.8 + - + -
249A VAL* 3.9 0.6 - - - +
250A ARG* 2.7 70.3 + - - +
251A ASP* 4.4 6.3 + - - +
252A THR* 4.2 3.6 - - - +
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE 3.0 13.3 + - - +
32A MET* 3.0 8.3 + - - +
34A ARG* 1.3 75.9 - - - +
36A MET* 1.3 64.0 + - - +
38A ASP* 3.1 3.8 + - - +
39A LEU* 2.9 42.1 + - + +
142A ILE* 4.0 21.3 - - + -
184A PHE* 3.9 17.0 - - + -
185A TYR* 4.1 13.5 - - + +
188A LEU* 4.3 8.7 - - + -
248A TYR* 3.8 37.5 - - + +
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Residues in contact with MET 36 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A MET 2.9 6.3 + - - +
33A LYS* 3.3 50.0 - - + +
35A VAL* 1.3 75.7 - - - +
37A LEU* 1.3 81.1 + - + +
39A LEU* 2.9 14.3 + - - +
40A LYS* 3.1 29.2 + - - +
93A ILE* 5.3 2.2 - - + -
142A ILE* 4.3 8.5 - - + +
143A LEU* 4.0 18.8 - - + +
146A TYR* 3.4 50.7 - - + -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LYS* 3.0 34.7 + - + +
34A ARG* 3.8 12.1 - - + +
35A VAL 3.4 0.2 - - - -
36A MET* 1.3 98.2 - - + +
38A ASP* 1.3 61.1 + - - +
40A LYS* 3.4 22.7 + - + +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG 3.0 14.4 + - - +
35A VAL 3.1 8.3 + - - +
37A LEU* 1.3 77.0 - - - +
39A LEU* 1.3 63.6 + - - +
40A LYS 3.6 4.2 + - - +
244A LYS* 4.6 10.4 + - - +
247A ASN* 5.0 9.8 + - - +
248A TYR* 2.5 33.7 + - + +
307A VAL* 5.4 7.4 - - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 2.9 36.2 + - + +
36A MET 2.9 3.6 + - - +
38A ASP* 1.3 79.2 - - + +
40A LYS* 1.3 66.7 + - - +
41A LYS* 4.0 13.8 + - - +
86A GLU* 4.6 0.2 - - - +
90A GLN* 3.1 17.5 + - - -
139A GLU* 3.6 61.7 - - + +
142A ILE* 4.7 3.6 - - + -
143A LEU* 3.5 23.1 - - + -
185A TYR* 5.4 2.0 - - - +
244A LYS* 6.2 2.2 - - - +
248A TYR* 5.2 5.4 - - - +
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Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MET* 3.1 38.0 + - - +
37A LEU* 3.5 20.5 - - + +
38A ASP 3.4 6.3 - - - +
39A LEU* 1.3 80.9 - - - +
41A LYS* 1.3 66.2 + - - +
42A PRO* 4.7 1.2 - - - +
46A MET* 5.3 0.8 - - - +
90A GLN* 3.8 9.6 + - - +
93A ILE* 4.2 26.1 + - + +
94A GLU* 3.1 43.1 + - - +
143A LEU* 5.0 0.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il